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Inhibition of Murine DNA Methyltransferase Dnmt3a by DNA Duplexes Containing Pyrimidine-2(1H)-one

N. A. Cherepanova1, A. L. Zhuze2, and E. S. Gromova1*

1Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: (495) 939-3181; E-mail: gromova@genebee.msu.ru; cherepanova@genebee.msu.ru

2Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, 119991 Moscow, Russia

* To whom correspondence should be addressed.

Received May 19, 2010; Revision received May 31, 2010
Here we studied the inhibition of the catalytic domain of Dnmt3a methyltransferase (Dnmt3a-CD) by DNA duplexes containing the mechanism-based inhibitor pyrimidine-2(1H)-one (P) instead of the target cytosine. It has been shown that conjugates of Dnmt3a-CD with P-DNA (DNA containing pyrimidine-2(1H)-one) are not stable to heating at 65°C in 0.1% SDS. The yield of covalent intermediate increases in the presence of the regulatory factor Dnmt3L. The importance of the DNA minor groove for covalent intermediate formation during the methylation reaction catalyzed by Dnmt3a-CD has been revealed. P-DNA was shown to inhibit Dnmt3a-CD; the IC50 is 830 nM. The competitive mechanism of inhibition of Dnmt3a-CD by P-DNA has been elucidated. It is suggested that therapeutic effect of zebularine could be achieved by inhibition of not only Dnmt1 but also Dnmt3a.
KEY WORDS: pyrimidine-2(1H)-one, covalent intermediate, competitive inhibition, eukaryotic DNA methyltransferase

DOI: 10.1134/S000629791009004X